Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/gff/VcfToGff.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
1 package gff;
2
3 import java.io.PrintStream;
4
5 import fileIO.ByteFile;
6 import fileIO.ByteStreamWriter;
7 import fileIO.FileFormat;
8 import shared.Parser;
9 import shared.PreParser;
10 import shared.ReadStats;
11 import shared.Timer;
12 import shared.Tools;
13 import structures.ByteBuilder;
14 import var2.VCFLine;
15
16 /**
17 * Stripped out of GffLine into independent class.
18 * @author Brian Bushnell
19 * @date Sep 12, 2018
20 *
21 */
22 public class VcfToGff {
23
24 /** Translates VCF to GFF */
25 public static void main(String[] args){
26 Timer t=new Timer();
27 PrintStream outstream=System.err;
28 {//Preparse block for help, config files, and outstream
29 PreParser pp=new PreParser(args, new Object() { }.getClass().getEnclosingClass(), false);
30 args=pp.args;
31 outstream=pp.outstream;
32 t.outstream=outstream;
33 }
34
35 Parser parser=new Parser();
36 String in=null;
37 String out=null;
38 boolean overwrite=true, append=false;
39
40 //Parse each argument
41 for(int i=0; i<args.length; i++){
42 String arg=args[i];
43
44 //Break arguments into their constituent parts, in the form of "a=b"
45 String[] split=arg.split("=");
46 String a=split[0].toLowerCase();
47 String b=split.length>1 ? split[1] : null;
48
49 if(a.equals("in") || a.equals("vcf")){
50 in=b;
51 }else if(a.equals("out") || a.equals("gff")){
52 out=b;
53 }else if(parser.parse(arg, a, b)){
54 //do nothing
55 }else if(in==null && b==null && i==0 && Tools.canRead(arg)){
56 in=arg;
57 }else if(in==null && b==null && i==1){
58 out=arg;
59 }else{
60 outstream.println("Unknown parameter "+args[i]);
61 assert(false) : "Unknown parameter "+args[i];
62 }
63 }
64
65 {//Process parser fields
66 overwrite=ReadStats.overwrite=parser.overwrite;
67 append=ReadStats.append=parser.append;
68 }
69
70 //Ensure output files can be written
71 if(!Tools.testOutputFiles(overwrite, append, false, out)){
72 outstream.println((out==null)+", "+out);
73 throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out+"\n");
74 }
75
76 //Ensure input files can be read
77 if(!Tools.testInputFiles(false, true, in)){
78 throw new RuntimeException("\nCan't read some input files.\n");
79 }
80
81 //Ensure that no file was specified multiple times
82 if(!Tools.testForDuplicateFiles(true, in, out)){
83 throw new RuntimeException("\nSome file names were specified multiple times.\n");
84 }
85
86 translate(in, out, overwrite, append);
87 t.stop("Time: \t");
88 }
89
90 /** Translates VCF to GFF */
91 private static void translate(String in, String out, boolean overwrite, boolean append){
92 //Create output FileFormat objects
93 FileFormat ffout=FileFormat.testOutput(out, FileFormat.GFF, "gff", true, overwrite, append, false);
94
95 //Create input FileFormat objects
96 FileFormat ffin=FileFormat.testInput(in, FileFormat.VCF, "vcf", true, true);
97
98 ByteFile bf=ByteFile.makeByteFile(ffin);
99 ByteStreamWriter bsw=null;
100 if(ffout!=null){
101 bsw=new ByteStreamWriter(ffout);
102 bsw.start();
103 }
104
105 ByteBuilder bb=new ByteBuilder(17000);
106 bb.append("##gff-version 3\n");
107 String header="#seqid source type start end score strand phase attributes";
108 for(byte[] line=bf.nextLine(); line!=null; line=bf.nextLine()){
109 if(line.length>1){
110 if(line[0]=='#'){
111 if(Tools.startsWith(line, "##fileformat") || Tools.startsWith(line, "##FORMAT") ||
112 Tools.startsWith(line, "##INFO") || Tools.startsWith(line, "#CHROM POS")){
113 //skip
114 }else{
115 int i=1;
116 while(i<line.length && line[i]=='#'){i++;}
117 i--;
118 bb.append(line, i, line.length-i);
119 bb.nl();
120 }
121 }else{
122 if(header!=null){
123 bb.append(header).append('\n');
124 header=null;
125 }
126 VCFLine vline=new VCFLine(line);
127 GffLine gline=new GffLine(vline);
128 gline.appendTo(bb);
129 bb.nl();
130 }
131 }
132 if(bb.length()>=16384){
133 if(bsw!=null){
134 bsw.print(bb);
135 }
136 bb.clear();
137 }
138 }
139 if(bb.length()>0){
140 if(bsw!=null){
141 bsw.print(bb);
142 }
143 bb.clear();
144 }
145 bf.close();
146 if(bsw!=null){bsw.poisonAndWait();}
147 }
148
149 }